Core Hopping

Improving the activity of a lead compound is often done by varying the side chains that are attached to a core part of the compound. The object of this strategy is to find the optimal side chains. Since in many cases it is the side chains that bind to the protein, it makes sense to vary the core, to find other molecules (“scaffolds”) to which the side chains could be attached and result in enhanced binding. This capability is available in the Core Hopping facility.

The core-hopping strategy is to screen multiple potential scaffolds (also called protocores) against a template (a lead compound), and search for alignments of potential attachment points on each scaffold with the attachment points on the template.

If a receptor is available, the core-hopping strategy can take advantage of the receptor by docking the new compounds into the binding site, and use the docking score to rate the compounds. If a receptor is not available, the new compounds can be rated on alignment alone or on the matching of the shape of the new compound to the template.

If you publish work that uses Core Hopping, please use the citation shown on our citation page.